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C&EN talks with Rommie Amaro, computational chemist: Amaro discusses how she uses molecular dynamics simulations to find new cancer drug leads

Determining the structures of enzymes and other biomolecules with X-ray crystallography has deepened biologists’ understanding of the inner workings of cells and led to the design of many important drugs. Increasingly, researchers are using computer modeling to attain a more realistic picture of the movement of these biomolecules in their natural environment. Rommie E. Amaro, a professor of chemistry and biochemistry at the University of California, San Diego (UCSD), uses computational techniques to predict how enzymes regularly shift their configurations, revealing potential vulnerable areas for drug targeting. C&EN talked with Amaro about how she’s using dynamic models of enzymes to develop a new class of cancer drugs, work that is being commercialized by Actavalon, a San Diego start-up Amaro cofounded. Link to the full article from the American Chemical Society

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Using data science to return people to the labor force: New center at Computation Institute to unify labor, training, education and employment data

Despite persistent unemployment in the United States, millions of jobs are hard to fill due to a lack of qualified applicants. While community college and training organizations seek to equip people with the skills required for these openings, it’s a moving target as the American economy rapidly changes. Link to the full article from The University of Chicago

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TSRI Scientists Awarded $6.6 Million for Research in Computational Biology

Three groups at The Scripps Research Institute (TSRI) have been awarded grants from the National Institutes of Health (NIH) to develop methods for computational modeling and to apply them to cutting-edge systems in biology and health. “The three projects are highly symbiotic, each addressing a different state-of-the-art challenge in computational biology, but built using a common computational framework that will allow facile collaboration between the groups,” said Professor Arthur Olson, founder of the Molecular Graphics Laboratory, which is currently part of the TSRI Department of Integrative Structural and Computational Biology. Link to the full article from the Scripps Research Institute

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Supercomputing the P53 protein as a promising anticancer therapy

Even though it's almost impossible to see, computational biophysicist Rommie Amaro is using the Stampede supercomputer at the Texas Advanced Computing Center at The University of Texas at Austin to model the largest atomic level system of the tumor suppression protein p53 to date — over 1.5 million atoms. The simulations identify new "pockets" to reactivate p53 which would be a tremendous boost for future anti-cancer drug iscovery. Link to full article from Texas Advanced Computing Center

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This protein is mutated in half of all cancers. New drugs aim to fix it before it’s too late

It has been nearly impossible to get a good look at Rommie Amaro's favorite protein in action. Called p53, the protein sounds the alarm to kill cells with DNA damage and prevent them from becoming cancerous—one reason why it has been called the "guardian of the genome." But it is big and floppy, a molecular shapeshifter that is hard to follow with standard imaging tools. So Amaro, a computational biologist at the University of California (UC), San Diego, turned to supercomputers. Link to the full article from the American Association for the Advancement of Science

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Science at cusp of 'transformational' grasp of life via cell modeling, researchers say

A paper recently published in the Journal of Molecular Biology shows how advances in molecular biology and computer science around the world soon may lead to a three-dimensional computer model of a cell, the fundamental unit of life. According to the authors, the development could herald a new era for biological research, medical science, and human and animal health. Link to the full article from Phys.org

 

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La Jollan wins top prize in Theoretical Chemistry

J. Andrew McCammon, a distinguished professor of chemistry, biochemistry and pharmacology at UC San Diego, has won the 2016-17 Joseph O. Hirschfelder Prize in Theoretical Chemistry, awarded by the Theoretical Chemistry Institute at the University of Wisconsin-Madison. A physical chemist who is also a fellow of the San Diego Supercomputer Center and a Howard Hughes Medical Institute Investigator, McCammon is the second UCSD chemistry professor to receive the prestigious prize, following Peter Wolynes in 2009. Link to the full article from the La Jolla Light 

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Promising drug leads

Using a unique computational approach to rapidly sample, in millisecond time intervals, proteins in their natural state of gyrating, bobbing, and weaving, a research team from UC San Diego and Monash University in Australia has identified promising drug leads that may selectively combat heart disease, from arrhythmias to cardiac failure. Please see links to a Full article in UC San Diego News Center and a published paper.

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Andrew McCammon is 2016-17 Hirschfelder Prize Recipient

Professor J. Andrew McCammon will receive the 2016-17 Joseph O. Hirschfelder Prize in Theoretical Chemistry, administered by the University of Wisconsin-Madison Theoretical Chemistry Institute (TCI). McCammon is a professor of chemistry, biochemistry, and pharmacology at the University of California, San Diego, where he holds the Joseph E. Mayer Chair of Theoretical Chemistry. He also is a member of the National Academy of Sciences and a fellow of the American Association for the Advancement of Science and the American Academy of Arts and Sciences. Link to the full article from the University of Wisconsin-Madison Department of Chemistry.

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Report from the Summer School in Computational Physiology

17 students attended this year's Summer School, a joint venture in Computational Physiology between the University of Oslo, University of California, San Diego, and Simula. The Summer School is now in its third year, and including this year's group we have a total of 44 graduates from the school. This summer, 15 of the students were PhDs and two were Master's students, selected from a pool of international applicants. Link to the full article from simula

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Computing transforms chemistry, biotech

The life sciences are going dry. While test tubes, Petri dishes and cell cultures abound in the biotech world, the frontiers of exploration are increasingly taking place on high-powered computers and supercomputers. Equipped with ever better microprocessors to perform calculations and render graphics, computers today run extraordinarily powerful software that sheds light on biomedicine at every scale — from the physics of atomic-level interactions to sophisticated models of how tissues function. Link to the full article from the San Diego Union Tribune

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Computer Simulations Aid Search for “Resistance-Resistant” Antibiotics

With the growing threat of drug-resistant bacterial infections, new antibiotics are sorely needed. But we need truly novel classes of antibiotics, not just new versions that kill bacteria the same singular way existing drugs do, says J. Andrew McCammon, PhD, Distinguished Professor of Pharmacology, Chemistry and Biochemistry, and Joseph E. Mayer Chair of Theoretical Chemistry at UC San Diego. We need “resistance-resistant” antibiotics — drugs bacteria won’t easily be able to ignore. Link to the full article at News from UC San Diego Health Sciences. 

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The recipe for Big Data

What do a cookbook and big data have to do with each other? Quite a bit, said Ilkay Altintas, the chief data science officer for the San Diego Supercomputer Center, motioning to the book “How to Cook Everything Fast,” which sits prominently on her office desk. Although it might seem like an odd choice of literature for Altintas, she sees it as central to her work. “That’s my dream project,” Altintas said. Link to the full article from UC San Diego Extension.

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Rommie Amaro: The Kavli Foundation Emerging Leader in Chemistry Lecture

Rommie Amaro giving the ACS Kavli Emerging Leader in Chemistry National Lecture at the Spring ACS.

Please see AMBER GPU MD workflow download links

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Rommie Amaro highlighted in Biophysics Week

The Biophysical Society’s Committees for Inclusion and Diversity (CID) and Professional Opportunities for Women (CPOW) have highlighted Rommie Amaro as an outstanding biophysicist who represent the diversity within the field.

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Andrew McCulloch’s article for Biophysics Week

Andrew McCulloch’s article about multiscale modeling for Biophysics Week!

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Ilkay Altintas wins the TCSC Award for Excellence

Ilkay Altintas wins the TCSC Award for Excellence in Scalable Computing for Early Career Researchers

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